Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004929.1 Hibiscus syriacus cultivar Beakdansim tig00011093_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 209567
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:188435 original size:33 final size:33
Alignment explanation
Indices: 188376--188460 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 33
188366 ACTAAATTCG
188376 CGTTGCGATTTTCATTTTCGCATTGCGATTCA-CT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATT-ATCT
*
188410 CGTTGCGATTTTCATTTCGCTTTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
**
188443 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
188461 CGCGTTGCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.02
33 32 0.68
34 14 0.30
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:188468 original size:20 final size:20
Alignment explanation
Indices: 188443--188511 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
188433 GCGATTATCT
188443 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
188463 CGTTGCAATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
188483 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
188503 CGTTGCGAT
1 CGTTGCGAT
188512 TTCCGCGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:188522 original size:34 final size:33
Alignment explanation
Indices: 188374--188530 Score: 111
Period size: 34 Copynumber: 4.5 Consensus size: 33
188364 AAACTAAATT
** *
188374 CGCGTTGCGATTTTCATTTTCGCATTGCGA-TTC
1 CGCGTTGCGATAGTCA-TTTCGCGTTGCGATTTC
* ** *
188407 ACTCGTTGCGATTTTCATTTCGCTTTGCGATTAT-
1 -CGCGTTGCGATAGTCATTTCGCGTTGCGATT-TC
*
188441 CTCGTTGCGATAGTCATTTCCGCGTTGCAATAGTCATTTC
1 CGCGTTGCGATAGTCATTT-CGCGTTGC----G--ATTTC
* *
188481 TGTGTTGCGATAGTCATATTCGCGTTGCGATTTC
1 CGCGTTGCGATAGTCAT-TTCGCGTTGCGATTTC
188515 CGCGTTGCGATAGTCA
1 CGCGTTGCGATAGTCA
188531 AATGAATGTC
Statistics
Matches: 102, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
33 29 0.28
34 42 0.41
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 25 0.25
41 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (33 bp):
CGCGTTGCGATAGTCATTTCGCGTTGCGATTTC
Found at i:191863 original size:20 final size:20
Alignment explanation
Indices: 191838--191903 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
191828 AAATTCAGTA
*
191838 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
191858 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
191878 TTGCGATAGTCAG-ATCTCG
1 TTGCGATAGTCAGAATCTCG
191897 TTGCGAT
1 TTGCGAT
191904 TTACAGATTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 13 0.29
20 32 0.71
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:191920 original size:39 final size:40
Alignment explanation
Indices: 191838--191923 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 40
191828 AAATTCAGTA
* **
191838 TTGCGATAGTTAGAATCTCGTTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGAG
* *
191878 TTGCGATAGTCAG-ATCTCGTTGCGAT-TTACAGATTCGAG
1 TTGCGATAGTCAGAATCTCGTTGCGATAGT-CAGAATCGAG
191917 TTGCGAT
1 TTGCGAT
191924 TTACGTATCG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
38 1 0.03
39 27 0.68
40 12 0.30
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (40 bp):
TTGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGAG
Found at i:191965 original size:20 final size:20
Alignment explanation
Indices: 191917--192044 Score: 170
Period size: 20 Copynumber: 6.5 Consensus size: 20
191907 CAGATTCGAG
191917 TTGCGATTTACGT-ATCGCA
1 TTGCGATTTACGTAATCGCA
191936 TTGC-ATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
191955 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
191975 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* ** *
191995 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACGTAA-TCGCA
* * *
192016 TTGCGATTTATGTATTCGCG
1 TTGCGATTTACGTAATCGCA
192036 TTGCGATTT
1 TTGCGATTT
192045 CGCATTGCGA
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
18 8 0.08
19 14 0.14
20 61 0.63
21 14 0.14
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:191993 original size:40 final size:40
Alignment explanation
Indices: 191917--192044 Score: 170
Period size: 41 Copynumber: 3.2 Consensus size: 40
191907 CAGATTCGAG
191917 TTGCGATTTACGT-ATCGCATTGC-ATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
191955 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
* ** * * * *
191995 TTGCGATTTTCCAAATTCGCGTTGCGATTTATGTATTCGCG
1 TTGCGATTTACGTAA-TCGCATTGCGATTTACGTAATCGCA
192036 TTGCGATTT
1 TTGCGATTT
192045 CGCATTGCGA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 13 0.16
39 10 0.12
40 27 0.34
41 30 0.38
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (40 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
Found at i:192075 original size:21 final size:21
Alignment explanation
Indices: 192051--192096 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
192041 ATTTCGCATT
192051 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
192072 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
192093 GCGA
1 GCGA
192097 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:207045 original size:22 final size:23
Alignment explanation
Indices: 207019--207079 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
207009 AGAACCCCAG
207019 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
207042 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
207064 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
207080 TCTGTACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Done.